3IRT Hydrolase, Ligase date Aug 24, 2009
title Crystal Structure Of The I93m Mutant Of Ubiquitin Carboxy-Te Hydrolase L1
authors C.W.Davies, T.K.Maiti, C.Das
compound source
Molecule: Ubiquitin Carboxyl-Terminal Hydrolase Isozyme L1
Chain: A, B
Synonym: Uch-L1, Ubiquitin Thioesterase L1, Neuron Cytoplas Protein 9.5, Pgp 9.5, Pgp9.5;
Ec: 3.4.19.12, 6.-.-.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pgp9.5, Uchl1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p-1
symmetry Space Group: P 4 21 2
R_factor 0.211 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
109.938 109.938 79.040 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand CL enzyme Hydrolase E.C.3.4.19.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceUbiquitin vinyl methyl ester binding orients the misaligned active site of the ubiquitin hydrolase UCHL1 into productive conformation., Boudreaux DA, Maiti TK, Davies CW, Das C, Proc Natl Acad Sci U S A. 2010 May 18;107(20):9117-22. Epub 2010 May 3. PMID:20439756
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (3irt.pdb1.gz) 37 Kb
  • Biological Unit Coordinates (3irt.pdb2.gz) 37 Kb
  • LPC: Ligand-Protein Contacts for 3IRT
  • CSU: Contacts of Structural Units for 3IRT
  • Structure Factors (90 Kb)
  • Retrieve 3IRT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3IRT from S2C, [Save to disk]
  • Re-refined 3irt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3IRT in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3IRT
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3IRT, from MSDmotif at EBI
  • Fold representative 3irt from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3irt_A] [3irt] [3irt_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3IRT
  • Community annotation for 3IRT at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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